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- PDB-6ipw: Crystal structure of CqsB2 from Streptomyces exfoliatus in comple... -

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Basic information

Entry
Database: PDB / ID: 6ipw
TitleCrystal structure of CqsB2 from Streptomyces exfoliatus in complex with the product, 1-(2-hydroxypropyl)-2-methyl-carbazole-3,4-dione
ComponentsCqsB2
KeywordsBIOSYNTHETIC PROTEIN / Carbazole biosynthesis / polyketide aromatase/cyclase
Function / homologySTART-like domain superfamily / Chem-AO6 / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTomita, T. / Kobayashi, M. / Nishiyama, M. / Kuzuyama, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces.
Authors: Kobayashi, M. / Tomita, T. / Shin-Ya, K. / Nishiyama, M. / Kuzuyama, T.
History
DepositionNov 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CqsB2
B: CqsB2
C: CqsB2
D: CqsB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6588
Polymers110,5804
Non-polymers1,0774
Water11,061614
1
A: CqsB2
B: CqsB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8294
Polymers55,2902
Non-polymers5392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-46 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: CqsB2
D: CqsB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8294
Polymers55,2902
Non-polymers5392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-40 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.227, 128.227, 125.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
CqsB2


Mass: 27645.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RILCodonPlus / References: UniProt: A0A5A4PV77*PLUS
#2: Chemical
ChemComp-AO6 / 2-methyl-1-[(2R)-2-oxidanylpropyl]-9H-carbazole-3,4-dione


Mass: 269.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence has been deposited to DDBJ with accession code LC406090.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl (pH8.5), 30% (w/v) PEG 4000, 0.2M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→125.43 Å / Num. obs: 61403 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.035 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.543 / Num. unique obs: 3009 / CC1/2: 0.948 / Rpim(I) all: 0.145

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IPV

6ipv


Resolution: 2.1→125.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.613 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22389 2903 4.7 %RANDOM
Rwork0.17794 ---
obs0.18009 58471 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.664 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→125.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 0 80 614 7906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197496
X-RAY DIFFRACTIONr_bond_other_d0.0020.026776
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.94410184
X-RAY DIFFRACTIONr_angle_other_deg0.8023.00315572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18423.878392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.925151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3641552
X-RAY DIFFRACTIONr_chiral_restr0.0790.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021824
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3452.333532
X-RAY DIFFRACTIONr_mcbond_other1.3412.333531
X-RAY DIFFRACTIONr_mcangle_it2.163.4874408
X-RAY DIFFRACTIONr_mcangle_other2.163.4874409
X-RAY DIFFRACTIONr_scbond_it1.6762.5263963
X-RAY DIFFRACTIONr_scbond_other1.6762.5273964
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7583.7065776
X-RAY DIFFRACTIONr_long_range_B_refined5.10920.3629689
X-RAY DIFFRACTIONr_long_range_B_other5.08820.3319650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 237 -
Rwork0.198 4186 -
obs--99.59 %

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